Transposase is a class of enzyme that binds to the ends of a transposon and catalyzes the movement of the transposon to another part of the genome by a cut and paste mechanism or a replicative transposition mechanism. These enzymes have been used in preparation of samples for next generation sequencing (NGS), mutagenesis, nucleic acid delivery (gene therapy), and generating pluripotent cells for regenerative medicine. In these applications, transposases do not act as isolated proteins, but act as nucleoproteins in complex with specific DNA sequences. Such sequences are commonly referred to as transposase recognition sequences, transposon ends, inverted repeat right (IRR), inverted repeat left (IRL), or adapters.
When used for NGS library preparation, transposase-adapter complexes are used to fragment genomic DNA, which is a crucial step to achieve high-throughput sequencing. Compared with other fragmentation techniques, such as sonication and DNAse treatment, transposase-based fragmentation allows many-fold save in time, labor and equipment expenditure taking into account that sample preparation constitutes about 50% of the overall sequencing costs. However, DNA fragmentation by currently available transposase-adapter complexes is less random. That is, it has bias resulting in more reads in some regions and less in others, which often results in 1-3% higher duplication rate and more sequencing effort to achieve the same overall coverage. Also conventional transposase-based NGS sample preparation methods require removal of adapters, which is time consuming, and are not suitable for processing samples with very low amount of DNAs.
Thus, there is also an un-met need for different transposase adapters with suitable activity and different properties so as to increase the randomness and reduce the duplication rate. There is an un-met need for methods that more efficient and/or suitable for direct processing in transposase reaction of samples with very low amount of DNAs.